Buggy code:
public class GitHubRepoCheck { public static void main ( final String [ ] args ) throws IOException , URISyntaxException , StudyImporterException { String arg = args [ 0 ] ; final File tmpDir = File . createTempFile ( "graph" , ".db" , FileUtils . getTempDirectory ( ) ) ; try { final GraphDatabaseService graphService = GraphService . getGraphService ( tmpDir . getAbsolutePath ( ) ) ; final StudyImporter importer = new GitHubImporterFactory ( ) . createImporter ( arg , new ParserFactoryImpl ( ) , new org . eol . globi . data . NodeFactoryImpl ( graphService ) ) ; importer . importStudy ( ) ; new NameResolver ( graphService ) . resolve ( ) ; <START_BUG> final ExecutionResult execute = new org . neo4j . cypher . javacompat . ExecutionEngine ( graphService ) . execute ( ( "START<seq2seq4repair_space>study<seq2seq4repair_space>=<seq2seq4repair_space>node:studies('*:*')<seq2seq4repair_space>" + ( ( ( ( ( ( ( ( ( ( "MATCH<seq2seq4repair_space>study-[:COLLECTED]->specimen-[:ORIGINALLY_DESCRIBED_AS]->origTaxon" + ",<seq2seq4repair_space>specimen-[inter]->otherSpecimen-[:ORIGINALLY_DESCRIBED_AS]->otherOrigTaxon" ) + ",<seq2seq4repair_space>specimen-[:CLASSIFIED_AS]->taxon" ) + ",<seq2seq4repair_space>otherSpecimen-[:CLASSIFIED_AS]->otherTaxon<seq2seq4repair_space>" ) + "<seq2seq4repair_space>WHERE<seq2seq4repair_space>not(has(inter.inverted))<seq2seq4repair_space>+<seq2seq4repair_space>" ) + "RETURN<seq2seq4repair_space>taxon.name<seq2seq4repair_space>as<seq2seq4repair_space>providedSourceTaxonName,<seq2seq4repair_space>taxon.externalId<seq2seq4repair_space>as<seq2seq4repair_space>providedSourceTaxonId" ) + ",<seq2seq4repair_space>taxon.name<seq2seq4repair_space>as<seq2seq4repair_space>resolvedSourceTaxonName,<seq2seq4repair_space>taxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>resolvedSourceTaxonId" ) + ",<seq2seq4repair_space>inter.iri<seq2seq4repair_space>as<seq2seq4repair_space>interactionTypeId,<seq2seq4repair_space>inter.label<seq2seq4repair_space>as<seq2seq4repair_space>interactionTypeLabel<seq2seq4repair_space>" ) + ",<seq2seq4repair_space>otherTaxon.name<seq2seq4repair_space>as<seq2seq4repair_space>providedTargetTaxonName,<seq2seq4repair_space>otherTaxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>providedTargetTaxonId" ) + ",<seq2seq4repair_space>otherTaxon.name<seq2seq4repair_space>as<seq2seq4repair_space>resolvedTargetTaxonName,<seq2seq4repair_space>otherTaxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>resolvedTargetTaxonId" ) + ",<seq2seq4repair_space>study.citation,<seq2seq4repair_space>study.source" ) ) ) ; <END_BUG> System . out . println ( execute . dumpToString ( ) ) ; } finally { FileUtils . deleteQuietly ( tmpDir ) ; } } }

Fix:
final ExecutionResult execute = new org . neo4j . cypher . javacompat . ExecutionEngine ( graphService ) . execute ( ( "START<seq2seq4repair_space>study<seq2seq4repair_space>=<seq2seq4repair_space>node:studies('*:*')<seq2seq4repair_space>" + ( ( ( ( ( ( ( ( ( ( "MATCH<seq2seq4repair_space>study-[:COLLECTED]->specimen-[:ORIGINALLY_DESCRIBED_AS]->origTaxon" + ",<seq2seq4repair_space>specimen-[inter]->otherSpecimen-[:ORIGINALLY_DESCRIBED_AS]->otherOrigTaxon" ) + ",<seq2seq4repair_space>specimen-[:CLASSIFIED_AS]->taxon" ) + ",<seq2seq4repair_space>otherSpecimen-[:CLASSIFIED_AS]->otherTaxon<seq2seq4repair_space>" ) + "<seq2seq4repair_space>WHERE<seq2seq4repair_space>not(has(inter.inverted))<seq2seq4repair_space>" ) + "RETURN<seq2seq4repair_space>taxon.name<seq2seq4repair_space>as<seq2seq4repair_space>providedSourceTaxonName,<seq2seq4repair_space>taxon.externalId<seq2seq4repair_space>as<seq2seq4repair_space>providedSourceTaxonId" ) + ",<seq2seq4repair_space>taxon.name<seq2seq4repair_space>as<seq2seq4repair_space>resolvedSourceTaxonName,<seq2seq4repair_space>taxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>resolvedSourceTaxonId" ) + ",<seq2seq4repair_space>inter.iri<seq2seq4repair_space>as<seq2seq4repair_space>interactionTypeId,<seq2seq4repair_space>inter.label<seq2seq4repair_space>as<seq2seq4repair_space>interactionTypeLabel<seq2seq4repair_space>" ) + ",<seq2seq4repair_space>otherTaxon.name<seq2seq4repair_space>as<seq2seq4repair_space>providedTargetTaxonName,<seq2seq4repair_space>otherTaxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>providedTargetTaxonId" ) + ",<seq2seq4repair_space>otherTaxon.name<seq2seq4repair_space>as<seq2seq4repair_space>resolvedTargetTaxonName,<seq2seq4repair_space>otherTaxon.externalId?<seq2seq4repair_space>as<seq2seq4repair_space>resolvedTargetTaxonId" ) + ",<seq2seq4repair_space>study.citation,<seq2seq4repair_space>study.source" ) ) ) ;